For some reason, the plugin behaves differently when called via the log import script and we get a fatal error.
PHP Fatal error: Cannot redeclare geoip_country_code_by_name() in /plugins/GeoIP/libs/geoip.inc on line 347
Checking if those functions have already been declared doesn't help as it seems the whole geoip.inc file shouldn't be called.
Piwik 1.8.2 mod_geoIP in Apache geoIP pecl extension in PHP
Please report the issue in the GeoIP ticket, thanks